Mercurial > repos > bgruening > hicexplorer_hicplottads

annotate hicPlotTADs.xml @ 4:50502e2beaaa draft

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planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
author iuc
date Sat, 16 Dec 2017 16:36:29 -0500
parents f23f7178fae6
children 144bf28956a7
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5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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1 <tool id="hicexplorer_hicplottads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
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2 <description>Plots the diagonal, and some values close to the diagonal of a HiC matrix</description>
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3 <macros>
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4 <token name="@BINARY@">hicPlotTADs</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10 sed '/^$/d' '$tracks_config' &&
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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11 @BINARY@
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12 --tracks '$tracks_config'
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13 #if $region and $region is not None:
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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14 --region '$region'
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15 #end if
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16 --outFileName plot.$image_file_format
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17 && mv plot.$image_file_format plot
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18 ]]>
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19 </command>
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20 <configfiles>
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21 <configfile name="tracks_config">
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22 #if $x_axis.x_axis_select == "yes":
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23 [x-axis]
1
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24 #if $x_axis.fontsize:
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25 fontsize = $x_axis.fontsize
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26 #end if
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27 #if $x_axis.where:
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28 where = $x_axis.where
1
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29 #end if
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30 #end if
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31 #for $counter, $track in enumerate($tracks):
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32 #if $track.track_file_style_conditional.track_file_style_selector == "hic_matrix_option":
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33 [hic_section_$counter]
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34 file = $track.track_file_style_conditional.track_input_h5
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35 file_type = hic_matrix
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36 title = $track.track_file_style_conditional.title
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37 #if $track.track_file_style_conditional.depth:
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38 depth = $track.track_file_style_conditional.depth
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39 #end if
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40 #if $track.track_file_style_conditional.colormap:
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41 colormap = $track.track_file_style_conditional.colormap
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42 #end if
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43 #if $track.track_file_style_conditional.min_value:
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44 min_value = $track.track_file_style_conditional.min_value
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45 #end if
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46 #if $track.track_file_style_conditional.max_value:
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47 max_value = $track.track_file_style_conditional.max_value
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48 #end if
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49 transform = $track.track_file_style_conditional.transform
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50 #if $track.track_file_style_conditional.boundaries_file:
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51 boundaries_file = $track.track_file_style_conditional.boundaries_file
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52 #end if
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53 #if $track.track_file_style_conditional.x_labels:
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54 x labels = $track.track_file_style_conditional.x_labels
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55 #end if
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56 #if $track.track_file_style_conditional.type:
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57 type = $track.track_file_style_conditional.type
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58 #end if
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59 #if $track.track_file_style_conditional.show_masked_bins:
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60 show_masked_bins = $track.track_file_style_conditional.show_masked_bins
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61 #end if
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62 #if $track.track_file_style_conditional.scale_factor:
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63 scale factor = $track.track_file_style_conditional.scale_factor
0
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64 #end if
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65
2
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66 #end if
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67 #if $track.track_file_style_conditional.track_file_style_selector == "tad_score_track_option":
0
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68
2
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69 [tad_score_$counter]
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70 file = $track.track_file_style_conditional.track_input_bedgraph
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71 title = $track.track_file_style_conditional.title
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72 #if $track.track_file_style_conditional.color:
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73 color = $track.track_file_style_conditional.color
0
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74 #end if
2
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75 #if $track.track_file_style_conditional.width_tad:
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76 width = $track.track_file_style_conditional.width_tad
1
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77 #end if
2
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78 #if $track.track_file_style_conditional.show_data:
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79 show data range = $track.track_file_style_conditional.show_data
0
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80 #end if
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81
2
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82 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
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83 #if $columns > 5:
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84 file_type = bedgraph_matrix
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85 #else:
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86 file_type = bedgraph
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87 #end if
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88 type = lines
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89 #end if
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90 #if $track.track_file_style_conditional.track_file_style_selector == "chrom_states_option":
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91
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92 [chrom states_$counter]
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93 file = $track.track_file_style_conditional.track_input_bed
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94 title = $track.track_file_style_conditional.title
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95 #if $track.track_file_style_conditional.color:
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96 color = $track.track_file_style_conditional.color
0
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97 #end if
2
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98 display = collapsed
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99 #if $track.track_file_style_conditional.width_chrom:
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100 width = $track.track_file_style_conditional.width_chrom
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101 #end if
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102 #if $track.track_file_style_conditional.border_color:
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103 border_color = $track.track_file_style_conditional.border_color
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104 #end if
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105 file_type = bed
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106 #end if
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107 #if $track.track_file_style_conditional.track_file_style_selector == "gene_track_option":
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108
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109 [genes_$counter]
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110 file = $track.track_file_style_conditional.track_input_bed
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111 title = $track.track_file_style_conditional.title
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112 #if $track.track_file_style_conditional.color:
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113 color = $track.track_file_style_conditional.color
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114 #end if
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115
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116 #if $track.track_file_style_conditional.width_bed:
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117 width = $track.track_file_style_conditional.width_bed
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118 #end if
0
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119
2
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120 #if $track.track_file_style_conditional.labels:
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121 labels = $track.track_file_style_conditional.labels
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122 #end if
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123
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124 #if $track.track_file_style_conditional.type:
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125 type = $track.track_file_style_conditional.type
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126 #end if
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127
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128 file_type = bed
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129 #if $track.track_file_style_conditional.fontsize:
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130 fontsize = $track.track_file_style_conditional.fontsize
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131 #end if
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132
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133 #if $track.track_file_style_conditional.gene_rows:
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134 gene rows = $track.track_file_style_conditional.gene_rows
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135 #end if
0
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136
2
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137 #if $track.track_file_style_conditional.global_max_row:
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138 global max row = $track.track_file_style_conditional.global_max_row
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139 #end if
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140
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141 #end if
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142
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143
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144 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_track_option":
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145
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146 [bedgraph_$counter]
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147 file = $track.track_file_style_conditional.track_input_bedgraph
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148 title = $track.track_file_style_conditional.title
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149 #if $track.track_file_style_conditional.color:
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150 color = $track.track_file_style_conditional.color
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151 #end if
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152 #if $track.track_file_style_conditional.width_bedgraph:
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153 width = $track.track_file_style_conditional.width_bedgraph
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154 #end if
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155 #if $track.track_file_style_conditional.show_data:
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156 show data range = $track.track_file_style_conditional.show_data
0
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157 #end if
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158
2
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159 #set $columns = len(open(str($track.track_file_style_conditional.track_input_bedgraph)).readline().split('\t'))
0
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160 #if $columns > 5:
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161 file_type = bedgraph_matrix
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162 #else:
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163 file_type = bedgraph
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164 #end if
2
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165 type = lines
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166 #end if
0
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167
2
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168 #if $track.track_file_style_conditional.track_file_style_selector == "bigwig_track_option":
0
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169
2
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170 [bigwig_$counter]
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171 file = $track.track_file_style_conditional.track_input_bigwig
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172 title = $track.track_file_style_conditional.title
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173 color = $track.track_file_style_conditional.color
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174 #if $track.track_file_style_conditional.min_value:
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175 min_value = $track.track_file_style_conditional.min_value
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176 #else:
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177 min_value = 0
0
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178 #end if
2
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179 #if $track.track_file_style_conditional.max_value:
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180 max_value = $track.track_file_style_conditional.max_value
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181 #else:
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182 max_value = auto
0
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183 #end if
2
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184 width = $track.track_file_style_conditional.width_bigwig
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185 #if $track.track_file_style_conditional.number_of_bins:
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186 number of bins = $track.track_file_style_conditional.number_of_bins
0
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187 #end if
2
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188 nans to zeros = $track.track_file_style_conditional.nans_to_zeros
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189 #if $track.track_file_style_conditional.type_conditional == 'fill_option':
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190 type = fill
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191 #elif $track.track_file_style_conditional.type_conditional == 'line_option':
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192 type = line:$track.track_file_style_conditional.type_conditional.width_line
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193 #elif $track.track_file_style_conditional.type_conditional == 'point_option':
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194 type = points:$track.track_file_style_conditional.type_conditional.width_point
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195 #end if
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196 #if $track.track_file_style_conditional.data_range:
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197 show data range = $track.track_file_style_conditional.data_range
0
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198 #end if
2
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199 file_type = bigwig
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200 #end if
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201 #if $track.track_file_style_conditional.track_file_style_selector == "bedgraph_matrix_track_option":
0
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202
2
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203 [bedgraph_matrix_$counter]
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204 file = $track.track_file_style_conditional.track_input_bedgraph_matrix
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205 title = $track.track_file_style_conditional.title
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206 #if $track.track_file_style_conditional.width_bedgraph:
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207 width = $track.track_file_style_conditional.width_bedgraph
0
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208 #end if
2
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209 orientation = inverted
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210 #if $track.track_file_style_conditional.min_value:
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211 min_value = $track.track_file_style_conditional.min_value
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212 #end if
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213 #if $track.track_file_style_conditional.max_value:
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214 max_value = $track.track_file_style_conditional.max_value
0
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215 #end if
2
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216 #if $track.track_file_style_conditional.type_lines:
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217 type = $track.track_file_style_conditional.type_lines
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218 #end if
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219 file_type = bedgraph_matrix
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220 plot horizontal lines=False
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221 #end if
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222 #if $track.track_file_style_conditional.track_file_style_selector == "vlines_track_option":
0
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223
2
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224 [vlines_$counter]
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225 file = $track.track_file_style_conditional.track_input_bed
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226 type = vlines
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227 file_type = bed
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228 #end if
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229 #if $track.track_file_style_conditional.track_file_style_selector == "spacer_option":
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230
0
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231 [spacer]
2
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232 #if $track.track_file_style_conditional.spacer_width:
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233 width = $track.track_file_style_conditional.spacer_width
0
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234 #end if
2
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235 #end if
0
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236 #end for</configfile>
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237 </configfiles>
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238 <inputs>
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239 <expand macro="region" />
2
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240
0
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241 <repeat name="tracks" min="1" title="Include tracks in your plot"
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242 help="Tracks can be of different filetypes. E.g BED, HiC-Matrix, BigWig or BedGraph">
2
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243 <conditional name="track_file_style_conditional">
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244 <param name="track_file_style_selector" type="select" label="Choose style of the track">
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245 <option value="hic_matrix_option">TAD visualization</option>
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246 <option value="chrom_states_option">Chromatine states</option>
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247 <option value="tad_score_track_option">TAD score</option>
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248 <option value="gene_track_option">Gene track</option>
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249 <option value="bigwig_track_option">Bigwig track</option>
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250 <option value="bedgraph_track_option">Bedgraph track </option>
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251 <option value="bedgraph_matrix_track_option">Bedgraph matrix track</option>
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252 <option value="vlines_track_option">Vlines track</option>
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253 <option value="spacer_option">Spacer</option>
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254 </param>
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255 <when value="hic_matrix_option">
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256 <expand macro="plot_title" />
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257 <expand macro="track_input_h5_macro" />
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258
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259 <expand macro="colormap" />
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260 <param name="depth" type="integer" value="8000000" optional="True" label="Depth" />
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261 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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262 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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263 <param name="transform" type="select" label="Plot the transformed value">
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264 <option value="log1p" selected="True" >log1p</option>
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265 <option value="log">log</option>
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266 <option value="-log">-log</option>
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267
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268 </param>
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269 <param name="type" type="select" optional="True" label="Plotting type">
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270 <option value="arcplot">arcplot</option>
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271 <option value="interaction">interaction</option>
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272 </param>
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273 <param name="show_masked_bins" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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274 label="Show masked bins" />
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275 <param name="boundaries_file" type="data" optional="True" format="bed" label="Boundaries file"/>
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276 <param name="scale_factor" type="float" value="1.0" optional="True" label="Scale factor" help="if the values in the matrix need to be scaled the following parameter can be used" />
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277 <param name="x_labels" type="boolean" truevalue="yes" falsevalue="no" optional="True" label="Show x labels" />
0
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278
2
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279 </when>
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280 <when value="tad_score_track_option">
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281 <expand macro="plot_title" />
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282 <expand macro="track_input_bedgraph_macro" />
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283 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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284
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285 <param name="width_tad" type="float" value="0.2" optional="True" label="Width"/>
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286 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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287 </when>
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288 <when value="chrom_states_option">
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289 <expand macro="plot_title" />
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290
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291 <expand macro="track_input_bed_macro" />
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292 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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293
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294 <param name="border_color" type="color" value="#000000" label="Border color" optional="True" />
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295 <param name="width_chrom" type="float" value="1.5" optional="True" label="Width"/>
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296 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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297 label="Plot labels" />
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298 </when>
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299 <when value="gene_track_option">
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300 <expand macro="plot_title" />
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301
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302 <expand macro="track_input_bed_macro" />
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303 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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304 <param name="width_bed" type="float" value="1.5" optional="True" label="Width"/>
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305 <param name="labels" type="boolean" truevalue="on" falsevalue="off" checked="true"
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306 label="Plot labels" />
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307 <param name="type" type="select" optional="True" label="Type">
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308 <option value="genes">genes</option>
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309 <option value="domains">domains</option>
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310 </param>
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311 <param name="global_max_row" type="boolean" truevalue="yes" falsevalue="no" checked="false"
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312 label="Global max rows" />
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313 <param name="gene_rows" type="integer" value="" optional="True" label="Gene rows" />
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314 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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315
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316 </when>
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317 <when value="bedgraph_track_option">
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318 <expand macro="plot_title" />
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319 <expand macro="track_input_bedgraph_macro" />
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320 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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321
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322 <param name="width_bedgraph" type="float" value="0.2" optional="True" label="Width"/>
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323 <param name='show_data' type="boolean" truevalue="yes" falsevalue="no" checked="false" optional="True" label="Show visualization of data range" />
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324 </when>
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325 <when value="bigwig_track_option">
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326 <expand macro="plot_title" />
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327
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328 <expand macro="track_input_bigwig_macro" />
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329 <param name="color" type="color" value="#000000" label="Color of track" optional="True" />
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330
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331 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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332 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
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333
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334 <param name="width_bigwig" type="float" value="1.5" optional="True" label="Width"/>
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335 <param name="number_of_bins" type="integer" value="" optional="True" label="Number of bins" />
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336 <param name="nans_to_zeros" type="boolean" truevalue="True" falsevalue="False" checked="false"
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337 label="NAN's to zeros" />
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338 <conditional name="type_conditional">
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339 <param name="type_selector" type="select" label="Choose style of the plot.">
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340 <option value="fill_option">fill</option>
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341 <option value="line_option">line</option>
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342 <option value="point_option">point</option>
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343 </param>
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344 <when value="line_option">
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345 <param name="width_line" type="float" value="0.5" optional="True" label="Width"/>
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346 </when>
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347 <when value="point_option">
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348 <param name="width_point" type="float" value="0.5" optional="True" label="Width"/>
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349 </when>
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350 <when value="fill_option" />
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351 </conditional>
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352 <param name="data_range" type="boolean" truevalue="yes" falsevalue="no" optional="True" checked="false" />
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353 </when>
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354
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355
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356 <when value="bedgraph_matrix_track_option">
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357 <expand macro="plot_title" />
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358
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359 <expand macro="track_input_bedgraph_matrix_macro" />
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360 <param name="min_value" type="float" value="" optional="True" label="Minimum value"/>
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361 <param name="max_value" type="float" value="" optional="True" label="Maximum value"/>
0
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362
2
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363 <param name="width_bedgraph" type="float" value="1.5" optional="True" label="Width"/>
0
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364
2
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365 <param name="type_lines" type="boolean" truevalue="lines" falsevalue="" checked="false"
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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366 label="Set 'type' to 'lines'" help="if type is set as lines, then the TAD score lines are drawn instead
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367 of the matrix set to lines if a heatmap representing the matrix is not wanted"/>
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368 </when>
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369 <when value="vlines_track_option">
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370 <expand macro="track_input_bed_macro" />
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371 </when>
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372 <when value="spacer_option">
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373 <expand macro="spacer_macro" />
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374 </when>
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375 </conditional>
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376
0
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377 </repeat>
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378
2
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379
0
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380 <conditional name="x_axis">
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381 <param name="x_axis_select" type="select" label="Configure x-axis">
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382 <option value="no" selected="True">No</option>
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383 <option value="yes">Yes</option>
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384 </param>
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385 <when value="yes">
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386 <param name="fontsize" type="integer" value="" optional="True" label="Fontsize" />
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387 <param name="where" type="select" optional="True" label="Where to place the x-axis">
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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388 <option value="top">Top</option>
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389 <option value="bottom">Bottom</option>
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390 </param>
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391 </when>
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392 <when value="no" />
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393 </conditional>
2
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394 <param name="image_file_format" type="select" label="Image output format">
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395 <option value="png">png</option>
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396 <option value="svg">svg</option>
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397 </param>
0
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398 </inputs>
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399 <outputs>
2
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400 <data format="png" name="outFileName" from_work_dir="plot">
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401 <change_format>
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402 <when input="image_file_format" value="png" format="png" />
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403 <when input="image_file_format" value="svg" format="svg" />
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404 </change_format>
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405 </data>
0
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406 </outputs>
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407 <tests>
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408 <test>
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409 <param name="region" value="chrX:3000000-3500000"/>
2
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410 <conditional name="x_axis">
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411 <param name="x_axis_select" value="yes" />
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412 </conditional>
0
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413 <repeat name="tracks">
2
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414 <conditional name="track_file_style_conditional">
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415 <param name="track_file_style_selector" value="hic_matrix_option" />
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416 <param name="track_input_h5" value="Li_et_al_2015.h5" ftype="h5" />
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417 <param name="title" value="Kc DpnII (Li et al. 2015)" />
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418 <param name="colormap" value="RdYlBu_r" />
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419 <param name="depth" value="200000" />
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420 <param name="transform" value="log1p" />
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421 <param name="boundaries_file" value="domains.bed" />
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422 <param name="x_labels" value="True" />
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423 </conditional>
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424 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
425 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
426 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
427 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
428 <param name="spacer_width" value="0.05" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
429 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
430 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
431 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
432 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
433 <param name="track_file_style_selector" value="chrom_states_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
434 <param name="track_input_bed" value="tad_classification.bed" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
435 <param name="title" value="TAD state" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
436 <param name="width_chrom" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
437 <param name="labels" value="off" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
438 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
439 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
440 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
441 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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442 <param name="track_file_style_selector" value="tad_score_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
443 <param name="track_input_bedgraph" value="tad_score.gz" ftype="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
444 <param name="title" value="TAD separation score (Ramirez et al.)" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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445 <param name="width_tad" value="10" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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446 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
447 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
448 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
449 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
450 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
451 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
452 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
453 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
454 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
455 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
456 <param name="track_file_style_selector" value="bedgraph_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
457 <param name="track_input_bedgraph" value="bedgraph_chrx_2e6_5e6.bg" ftype="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
458 <param name="title" value="bedgraph" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
459 <param name="width_bedgraph" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
460 <param name="color" value="blue" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
461 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
462 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
bgruening
parents:
diff changeset
463 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
464 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
465 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
466 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
467 <param name="title" value="rep 1 test fill" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
468 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
469 <param name="color" value="blue" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
470 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
471 <param name="type_selector" value="fill_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
472 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
473 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
474 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
475
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
476 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
477 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
478 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
479 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
480 <param name="title" value="rep 1 test line" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
481 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
482 <param name="color" value="red" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
483 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
484 <param name="type_selector" value="line_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
485 <param name="width_line" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
486 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
487 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
488 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
489
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
490 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
491 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
492 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
493 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
494 <param name="title" value="rep 1 test lw=0.2" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
495 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
496 <param name="color" value="red" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
497 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
498 <param name="type_selector" value="line_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
499 <param name="width_line" value="0.1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
500
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
501 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
502 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
503 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
504
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
505 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
506 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
507 <param name="track_file_style_selector" value="bigwig_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
508 <param name="track_input_bigwig" value="bigwig_chrx_2e6_5e6.bw" ftype="bigwig" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
bgruening
parents: 1
diff changeset
509 <param name="title" value="rep 1 test point:0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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510 <param name="width_bigwig" value="4" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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511 <param name="color" value="black" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
512 <conditional name="type_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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513 <param name="type_selector" value="point_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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514 <param name="width_point" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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515
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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516 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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517 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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518 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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519
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
520 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
521 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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522 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
523 <param name="spacer_width" value="0.5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
524 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
525 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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parents:
diff changeset
526 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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527 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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528 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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529 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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530 <param name="title" value="genes" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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diff changeset
531 <param name="width_bed" value="5" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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532 <param name="fontsize" value="10" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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533 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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534 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
535 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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536 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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537 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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538 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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539 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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540 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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541 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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542 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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543 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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544 <param name="track_input_bed" value="dm3_genes.bed.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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545 <param name="title" value="max num rows 3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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546 <param name="width_bed" value="3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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547 <param name="fontsize" value="8" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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548 <param name="gene_rows" value="3" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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549 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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550 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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551 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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552 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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553 <param name="track_file_style_selector" value="spacer_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
diff changeset
554 <param name="spacer_width" value="1" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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555 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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diff changeset
556 </repeat>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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557 <repeat name="tracks">
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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558 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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559 <param name="track_file_style_selector" value="gene_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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560 <param name="track_input_bed" value="dm3_genes.bed6.gz" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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561 <param name="title" value="bed6 global max row" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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parents: 1
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562 <param name="width_bed" value="20" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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563 <param name="fontsize" value="10" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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564 <param name="global_max_row" value="True" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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565 </conditional>
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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566 </repeat>
2
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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567 <repeat name="tracks">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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568 <conditional name="track_file_style_conditional">
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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569 <param name="track_file_style_selector" value="vlines_track_option" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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570 <param name="track_input_bed" value="domains.bed" ftype="bed" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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571 <param name="type" value="vlines" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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572 </conditional>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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573 </repeat>
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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574 <param name="image_file_format" value="png" />
f23f7178fae6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 4d61b6bf2fed275ab38c226d0c4390b095a38251
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575 <output name="outFileName" file="master_TADs_plot.png" ftype="png" compare="sim_size" delta="35000" />
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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576 </test>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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577 </tests>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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578 <help><![CDATA[
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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579
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
580 Plot TADs
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
581 =========
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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582
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
583 ``hicPlotTADs`` is a visualization tool to plot the topologically associating domains (TADs) in a given region. Additional tracks can be added to enable the comparisons with other data like gene tracks.
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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584
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
585 Input
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
586 -----
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
587 - the region to plot: chr1:1000-2000
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
588 - the tracks:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
589 - the contact matrix
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
590 - Boundaries file: The result of ``hicFindTADs``.
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
591 - different tracks for comparison:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
592 - Chromatine states:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
593 - TAD score
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
594 - gene tracks
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
diff changeset
595 - Generic bigwig, bedgraph or bedgraph matrix files
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
iuc
parents: 2
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596 - Vlines: vertical lines as a visual support where regions start / end over all tracks
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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597 - Spacer: Add some space between the different tracks
0
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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598
4
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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599 For each track parameters for the color, the width or the font size can be defined.
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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600
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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601 Output
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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602 ------
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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603 An output looks like this:
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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604
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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605
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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606 .. image:: $PATH_TO_IMAGES/master_TADs_plot.png
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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607 :width: 80 %
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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608
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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609 | For more information about HiCExplorer please consider our documentation on readthedocs.io_
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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610
50502e2beaaa planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit dfa5a68cb20842407941c7ffda9ef956a0e86a04
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611 .. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
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612 ]]></help>
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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613 <expand macro="citations" />
5e0a39c5bcf6 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04
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614 </tool>